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Merge pull request #238 from CanDIG/sonchau/curator
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DIG-1663: Allow program curators to ingest/delete
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@SonQBChau
SonQBChau authored Jul 5, 2024
2 parents 1c25362 + 63dfbd8 commit e45dd4e
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Showing 15 changed files with 522 additions and 170 deletions.
66 changes: 16 additions & 50 deletions chord_metadata_service/mohpackets/apis/clinical_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,24 +92,6 @@ def wrapper(request, filters):
return wrapper


##########################################
# #
# DELETE FUNCTIONS #
# #
##########################################
@router.delete(
"/program/{program_id}/",
response={204: None, 404: Dict[str, str]},
)
def delete_program(request, program_id: str):
try:
dataset = Program.objects.get(pk=program_id)
dataset.delete()
return HTTPStatus.NO_CONTENT, None
except Program.DoesNotExist:
return HTTPStatus.NOT_FOUND, {"error": "Program matching query does not exist"}


##########################################
# #
# DONOR WITH CLINICAL DATA #
Expand All @@ -120,9 +102,8 @@ def delete_program(request, program_id: str):
response={200: DonorWithClinicalDataSchema, 404: Dict[str, str]},
)
def get_donor_with_clinical_data(request, program_id: str, donor_id: str):
authorized_datasets = request.authorized_datasets
q = (
Q(program_id__in=authorized_datasets)
Q(program_id__in=request.read_datasets)
& Q(program_id=program_id)
& Q(submitter_donor_id=donor_id)
)
Expand Down Expand Up @@ -175,16 +156,14 @@ def get_donor_with_clinical_data(request, program_id: str, donor_id: str):
response=List[ProgramModelSchema],
)
def list_programs(request, filters: Query[ProgramFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Program.objects.filter(q)


@router.get("/donors/", response=List[DonorModelSchema])
def list_donors(request, filters: Query[DonorFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Donor.objects.filter(q)

Expand All @@ -201,8 +180,7 @@ def check_filter_donor_with_program(filters):
response=List[PrimaryDiagnosisModelSchema],
)
def list_primary_diagnoses(request, filters: Query[PrimaryDiagnosisFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return PrimaryDiagnosis.objects.filter(q)

Expand All @@ -212,8 +190,7 @@ def list_primary_diagnoses(request, filters: Query[PrimaryDiagnosisFilterSchema]
response=List[BiomarkerModelSchema],
)
def list_biomarkers(request, filters: Query[BiomarkerFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Biomarker.objects.filter(q)

Expand All @@ -223,8 +200,7 @@ def list_biomarkers(request, filters: Query[BiomarkerFilterSchema]):
response=List[ChemotherapyModelSchema],
)
def list_chemotherapies(request, filters: Query[ChemotherapyFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Chemotherapy.objects.filter(q)

Expand All @@ -234,8 +210,7 @@ def list_chemotherapies(request, filters: Query[ChemotherapyFilterSchema]):
response=List[ComorbidityModelSchema],
)
def list_comorbidities(request, filters: Query[ComorbidityFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Comorbidity.objects.filter(q)

Expand All @@ -245,8 +220,7 @@ def list_comorbidities(request, filters: Query[ComorbidityFilterSchema]):
response=List[ExposureModelSchema],
)
def list_exposures(request, filters: Query[ExposureFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Exposure.objects.filter(q)

Expand All @@ -256,8 +230,7 @@ def list_exposures(request, filters: Query[ExposureFilterSchema]):
response=List[FollowUpModelSchema],
)
def list_follow_ups(request, filters: Query[FollowUpFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return FollowUp.objects.filter(q)

Expand All @@ -267,8 +240,7 @@ def list_follow_ups(request, filters: Query[FollowUpFilterSchema]):
response=List[HormoneTherapyModelSchema],
)
def list_hormone_therapies(request, filters: Query[HormoneTherapyFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return HormoneTherapy.objects.filter(q)

Expand All @@ -278,8 +250,7 @@ def list_hormone_therapies(request, filters: Query[HormoneTherapyFilterSchema]):
response=List[ImmunotherapyModelSchema],
)
def list_immunotherapies(request, filters: Query[ImmunotherapyFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Immunotherapy.objects.filter(q)

Expand All @@ -289,8 +260,7 @@ def list_immunotherapies(request, filters: Query[ImmunotherapyFilterSchema]):
response=List[RadiationModelSchema],
)
def list_radiations(request, filters: Query[RadiationFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Radiation.objects.filter(q)

Expand All @@ -300,8 +270,7 @@ def list_radiations(request, filters: Query[RadiationFilterSchema]):
response=List[SampleRegistrationModelSchema],
)
def list_sample_registrations(request, filters: Query[SampleRegistrationFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return SampleRegistration.objects.filter(q)

Expand All @@ -311,8 +280,7 @@ def list_sample_registrations(request, filters: Query[SampleRegistrationFilterSc
response=List[SpecimenModelSchema],
)
def list_specimens(request, filters: Query[SpecimenFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Specimen.objects.filter(q)

Expand All @@ -322,8 +290,7 @@ def list_specimens(request, filters: Query[SpecimenFilterSchema]):
response=List[SurgeryModelSchema],
)
def list_surgeries(request, filters: Query[SurgeryFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Surgery.objects.filter(q)

Expand All @@ -333,7 +300,6 @@ def list_surgeries(request, filters: Query[SurgeryFilterSchema]):
response=List[TreatmentModelSchema],
)
def list_treatments(request, filters: Query[TreatmentFilterSchema]):
authorized_datasets = request.authorized_datasets
q = Q(program_id__in=authorized_datasets)
q = Q(program_id__in=request.read_datasets)
q &= filters.get_filter_expression()
return Treatment.objects.filter(q)
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